Campaign 2016 (PhD Chapter 1)

1. Maps
- 1.1. General map
- 1.2. Parameters maps
2. Figures

This series of files compile all analyses done during Chapter 1 for the regional campaign of 2016.

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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To assess analyses and regressions, click here.
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Caracteristics of each campaign

		2014	2016	2017
Sampling date		August-September	June to August	July
Criteria for perturbation		Potentially impacted if close to the city or industries, References outside the bay	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered		BSI	BSI, CPC, BDA, MR	BSI, MR
Number of sampled stations		40 (20 HI, 20 R)	78 (26 BSI, 19 CPC, 18 BDA, 15 MR)	126 (111 BSI, 15 MR)
Parameters sampled	Organic matter	yes	yes	yes
	Photosynthetic pigments	no	yes	yes
	Sediment grain-size	yes	yes	yes
	Heavy-metals	yes	yes (for a limited number of stations)	no (interpolated based on 2014 and 2016 values)
Benthic communities	Compartment targeted	Macro-infauna	Macro-infauna	Macro-infauna
	Sieved used	500 µm	1 mm	500 µm and 1 mm
	Conservation technique	Formaldehyle	Formaldehyle	Formaldehyle
Others		N.A.	N.A.	N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Depth of the station: depth (only for ANCOVAs)
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Species richness: S
Abundance of total individuals: N
Shannon index: H
Piélou evenness: J

Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).

As data is missing for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, CPC, BDA, MR with habitat parameters
Design 2: stations at BSI with heavy metal concentrations.

Statistics for each variable considered:

BSI, CPC, BDA, MR (without heavy metals)
	Mean	SD	SE	Median	Min	Max	95% CI
depth	20.362	16.975	1.947	15.500	1.000	65.900	3.816
om	0.691	0.738	0.085	0.384	0.168	3.863	0.166
gravel	0.046	0.118	0.014	0.000	0.000	0.809	0.027
sand	0.707	0.352	0.040	0.883	0.000	1.001	0.079
silt	0.203	0.288	0.033	0.031	0.000	0.942	0.065
clay	0.044	0.099	0.011	0.006	0.000	0.497	0.022
S	4.671	2.895	0.332	4.000	0.000	13.000	0.651
N	19.408	25.758	2.955	12.000	0.000	142.000	5.791
H	1.059	0.603	0.069	1.025	0.000	2.307	0.136
J	0.721	0.295	0.034	0.838	0.000	1.000	0.066

BSI (only heavy metals)
	Mean	SD	SE	Median	Min	Max	95% CI
arsenic	4.300	4.759	0.971	2.500	0.800	21.300	1.904
cadmium	0.153	0.048	0.010	0.145	0.080	0.270	0.019
chromium	49.667	24.539	5.009	40.500	17.000	111.000	9.817
copper	9.787	7.764	1.585	7.800	2.400	28.800	3.106
iron	45356.633	17343.813	3540.291	39733.450	21938.100	85408.600	6938.843
manganese	776.663	362.884	74.073	677.850	318.400	1657.100	145.181
mercury	0.023	0.017	0.004	0.019	0.007	0.091	0.007
lead	5.421	3.021	0.617	4.650	1.900	12.200	1.209
zinc	59.358	30.340	6.193	47.700	26.900	141.400	12.138

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Conditions

Phylum abundances by condition
Phylum	HI	R
Annelida	275	231
Echinodermata	230	162
Mollusca	196	189
Arthropoda	110	73
Platyhelminthes	3	0
Nematoda	1	0
Nemertea	1	0
Brachiopoda	0	2
Cnidaria	0	2

Regions

Phylum abundances by region
Phylum	BSI	CPC	BDA	MR
Annelida	206	69	188	43
Mollusca	151	45	89	100
Arthropoda	97	13	30	43
Echinodermata	24	206	24	138
Platyhelminthes	3	0	0	0
Nematoda	1	0	0	0
Nemertea	1	0	0	0
Brachiopoda	0	0	0	2
Cnidaria	0	0	0	2